simbad.mr.phaser_mr module¶

Module to run phaser on a model

class Phaser(enant, hklin, hklout, i, logfile, nmol, pdbin, pdbout, sigi, solvent, timeout, work_dir)[source]¶

Bases: object

Class to run PHASER

Examples

>>> from simbad.mr.phaser_mr import Phaser
>>> phaser = Phaser('<enant>', '<hklin>', '<hklout>', '<i>', '<logfile>', '<nmol>', '<pdbin>', '<pdbout>', '<sigi>',
>>>                 '<solvent>', '<timeout>', '<workdir>')
>>> phaser.run()

Files relating to the PHASER run will be contained within the work_dir however the location of the output hkl, pdb and logfile can be specified.

Attributes:

enant : bool Whether to check for enantimophic space groups f : str The column label for F hklin : str The input hkl file hklout : str The output hkl file logfile : str The logfile output pdbin : str The input pdb file pdbout : str The output pdb file sigf : str The column label for SIGF solvent : int float The estimated solvent content of the crystal work_dir : str Path to the working directory were you want PHASER to run

Methods

phaser(logfile, key)	Function to run molecular replacement using PHASER
run()	Function to run molecular replacement using PHASER

enant¶

Whether to check for enantimophic space groups

hklin¶

The input hkl file

hklout¶

The output hkl file

i¶

The I label from the input hkl

logfile¶

The logfile output

nmol¶

The number of molecules to look for

pdbin¶

The input pdb file

pdbout¶

The output pdb file

static phaser(logfile, key)[source]¶

Function to run molecular replacement using PHASER

Parameters:	logfile : str Path to the output log file key : str PHASER keywords
Returns:	file Output hkl file file Output pdb file file Output log file

run()[source]¶

Function to run molecular replacement using PHASER

Returns:	file Output hkl file file Output pdb file file Output log file

sigi¶

The SIGI label from the input hkl

solvent¶

The estimated solvent content of the crystal

timeout¶

The time in minutes before phaser is killed